Stereospecific assignment of the asparagine and glutamine sidechain amide protons in proteins from chemical shift analysis
Stereospecific assignment of the asparagine and glutamine sidechain amide protons in proteins from chemical shift analysis
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DOI：
10.1007/s10858-017-0093-x
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发表时间：
2017-02-01
影响因子：
2.7
通讯作者：
Kalbitzer, Hans Robert
中科院分区：
文献类型：
--
作者：
Harsch, Tobias;Schneider, Philipp;Kalbitzer, Hans Robert
无规卷曲肽中天冬酰胺和谷氨酰胺残基的侧链酰胺质子的特征在于大的化学位移差异，并且可以仅基于其化学位移值进行立体特异性分配。存储在生物磁共振数据库（BMRB）的双峰化学位移分布不允许这样的分配。然而，对BMRB的分析表明，所有存储的立体特异性分配的相当大的一部分是不正确的。我们在这里表明，在大多数情况下，立体专一性分配也可以使用无偏的人工化学位移数据库（UACSB）的折叠蛋白质。对于天冬酰胺差异>0.40 ppm和谷氨酰胺差异>0.42 ppm的两条酰胺共振线的化学位移分离，低场位移共振线可以分别归属于H-δ 21和H-δ 21，置信水平> 95%。从UASCB导出的分类器也可以用于校正BMRB数据。在AUREML中实现的程序工具Assignmentalgorithm计算给定立体特异性分配的贝叶斯概率，并自动校正给定化学位移列表的分配。
Side chain amide protons of asparagine and glutamine residues in random-coil peptides are characterized by large chemical shift differences and can be stereospecifically assigned on the basis of their chemical shift values only. The bimodal chemical shift distributions stored in the biological magnetic resonance data bank (BMRB) do not allow such an assignment. However, an analysis of the BMRB shows, that a substantial part of all stored stereospecific assignments is not correct. We show here that in most cases stereospecific assignment can also be done for folded proteins using an unbiased artificial chemical shift data base (UACSB). For a separation of the chemical shifts of the two amide resonance lines with differences >0.40 ppm for asparagine and differences >0.42 ppm for glutamine, the downfield shifted resonance lines can be assigned to H-delta 21 and H-epsilon 21, respectively, at a confidence level > 95%. A classifier derived from UASCB can also be used to correct the BMRB data. The program tool AssignmentChecker implemented in AUREMOL calculates the Bayesian probability for a given stereospecific assignment and automatically corrects the assignments for a given list of chemical shifts.